Human Gene NHLH2 (ENST00000320238.3_7) from GENCODE V47lift37
  Description: nescient helix-loop-helix 2, transcript variant 1 (from RefSeq NM_005599.3)
Gencode Transcript: ENST00000320238.3_7
Gencode Gene: ENSG00000177551.5_10
Transcript (Including UTRs)
   Position: hg19 chr1:116,378,998-116,383,747 Size: 4,750 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:116,380,586-116,380,993 Size: 408 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:116,378,998-116,383,747)mRNA (may differ from genome)Protein (135 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HEN2_HUMAN
DESCRIPTION: RecName: Full=Helix-loop-helix protein 2; Short=HEN-2; AltName: Full=Class A basic helix-loop-helix protein 34; Short=bHLHa34; AltName: Full=Nescient helix loop helix 2; Short=NSCL-2;
FUNCTION: May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein.
INTERACTION: Q96EB6:SIRT1; NbExp=2; IntAct=EBI-5378683, EBI-1802965;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NHLH2
Diseases sorted by gene-association score: neuroblastoma (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.24 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 14.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -113.30516-0.220 Picture PostScript Text
3' UTR -452.401588-0.285 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q02577
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007417 central nervous system development
GO:0007617 mating behavior
GO:0030154 cell differentiation
GO:0042698 ovulation cycle
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  M96740 - Human NSCL-2 gene sequence.
AK056621 - Homo sapiens cDNA FLJ32059 fis, clone NTONG2001676, highly similar to HELIX-LOOP-HELIX PROTEIN 2.
AK307156 - Homo sapiens cDNA, FLJ97104.
BC096359 - Homo sapiens nescient helix loop helix 2, mRNA (cDNA clone MGC:117066 IMAGE:40010648), complete cds.
BC096360 - Homo sapiens nescient helix loop helix 2, mRNA (cDNA clone MGC:117067 IMAGE:40010649), complete cds.
AK312849 - Homo sapiens cDNA, FLJ93291, highly similar to Homo sapiens nescient helix loop helix 2 (NHLH2), mRNA.
KJ891703 - Synthetic construct Homo sapiens clone ccsbBroadEn_01097 NHLH2 gene, encodes complete protein.
AB587596 - Synthetic construct DNA, clone: pF1KB9626, Homo sapiens NHLH2 gene for nescient helix loop helix 2, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHA34, ENST00000320238.1, ENST00000320238.2, HEN2, HEN2_HUMAN, KIAA0490, NM_005599, Q02577, Q5T1P6, uc317qvb.1, uc317qvb.2
UCSC ID: ENST00000320238.3_7
RefSeq Accession: NM_005599.3
Protein: Q02577 (aka HEN2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.